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Items: 1 to 20 of 125

1.

Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium.

Grove ML, Yu B, Cochran BJ, Haritunians T, Bis JC, Taylor KD, Hansen M, Borecki IB, Cupples LA, Fornage M, Gudnason V, Harris TB, Kathiresan S, Kraaij R, Launer LJ, Levy D, Liu Y, Mosley T, Peloso GM, Psaty BM, Rich SS, Rivadeneira F, Siscovick DS, Smith AV, Uitterlinden A, van Duijn CM, Wilson JG, O'Donnell CJ, Rotter JI, Boerwinkle E.

PLoS One. 2013 Jul 12;8(7):e68095. doi: 10.1371/journal.pone.0068095. Print 2013.

2.

iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array.

Zhou J, Tantoso E, Wong LP, Ong RT, Bei JX, Li Y, Liu J, Khor CC, Teo YY.

Bioinformatics. 2014 Jun 15;30(12):1714-20. doi: 10.1093/bioinformatics/btu107. Epub 2014 Feb 23.

PMID:
24567545
3.

Imputation-based assessment of next generation rare exome variant arrays.

Martin AR, Tse G, Bustamante CD, Kenny EE.

Pac Symp Biocomput. 2014:241-52.

4.

A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data.

Kim YJ, Lee J, Kim BJ; T2D-Genes Consortium, Park T.

BMC Genomics. 2015 Dec 29;16:1109. doi: 10.1186/s12864-015-2192-y.

5.

Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population.

Park TJ, Heo L, Moon S, Kim YJ, Oh JH, Han S, Kim BJ.

Int J Genomics. 2015;2015:421715. doi: 10.1155/2015/421715. Epub 2015 Dec 27.

6.

Comparison of genotype clustering tools with rare variants.

Perreault LP, Legault MA, Barhdadi A, Provost S, Normand V, Tardif JC, Dubé MP.

BMC Bioinformatics. 2014 Feb 21;15:52. doi: 10.1186/1471-2105-15-52.

7.

Quality Control for the Illumina HumanExome BeadChip.

Igo RP Jr, Cooke Bailey JN, Romm J, Haines JL, Wiggs JL.

Curr Protoc Hum Genet. 2016 Jul 1;90:2.14.1-2.14.16. doi: 10.1002/cphg.15.

8.

Joint genotype calling with array and sequence data.

O'Connell J, Marchini J.

Genet Epidemiol. 2012 Sep;36(6):527-37. doi: 10.1002/gepi.21657. Epub 2012 Jul 20.

PMID:
22821426
9.

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

Hong H, Su Z, Ge W, Shi L, Perkins R, Fang H, Xu J, Chen JJ, Han T, Kaput J, Fuscoe JC, Tong W.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S17. doi: 10.1186/1471-2105-9-S9-S17.

10.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE.

BMC Genomics. 2012 Dec 6;13:683. doi: 10.1186/1471-2164-13-683.

11.

A genotype calling algorithm for the Illumina BeadArray platform.

Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP, Clark TG.

Bioinformatics. 2007 Oct 15;23(20):2741-6. Epub 2007 Sep 10.

12.

Assessing the Power of Exome Chips.

Page CM, Baranzini SE, Mevik BH, Bos SD, Harbo HF, Andreassen BK.

PLoS One. 2015 Oct 5;10(10):e0139642. doi: 10.1371/journal.pone.0139642. eCollection 2015.

13.

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.

Trubetskoy V, Rodriguez A, Dave U, Campbell N, Crawford EL, Cook EH, Sutcliffe JS, Foster I, Madduri R, Cox NJ, Davis LK.

Bioinformatics. 2015 Jan 15;31(2):187-93. doi: 10.1093/bioinformatics/btu591. Epub 2014 Sep 29.

14.

zCall: a rare variant caller for array-based genotyping: genetics and population analysis.

Goldstein JI, Crenshaw A, Carey J, Grant GB, Maguire J, Fromer M, O'Dushlaine C, Moran JL, Chambert K, Stevens C; Swedish Schizophrenia Consortium; ARRA Autism Sequencing Consortium, Sklar P, Hultman CM, Purcell S, McCarroll SA, Sullivan PF, Daly MJ, Neale BM.

Bioinformatics. 2012 Oct 1;28(19):2543-5. Epub 2012 Jul 27.

15.

SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

Huentelman MJ, Craig DW, Shieh AD, Corneveaux JJ, Hu-Lince D, Pearson JV, Stephan DA.

BMC Genomics. 2005 Oct 31;6:149.

16.

optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.

Shah TS, Liu JZ, Floyd JA, Morris JA, Wirth N, Barrett JC, Anderson CA.

Bioinformatics. 2012 Jun 15;28(12):1598-603. doi: 10.1093/bioinformatics/bts180. Epub 2012 Apr 12.

17.

Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys.

Rincon G, Weber KL, Eenennaam AL, Golden BL, Medrano JF.

J Dairy Sci. 2011 Dec;94(12):6116-21. doi: 10.3168/jds.2011-4764.

PMID:
22118099
18.

Chip-based direct genotyping of coding variants in genome wide association studies: utility, issues and prospects.

Nievergelt CM, Wineinger NE, Libiger O, Pham P, Zhang G, Baker DG; Marine Resiliency Study Investigators, Schork NJ.

Gene. 2014 Apr 25;540(1):104-9. doi: 10.1016/j.gene.2014.01.069. Epub 2014 Feb 9.

19.

Illumina human exome genotyping array clustering and quality control.

Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J.

Nat Protoc. 2014 Nov;9(11):2643-62. doi: 10.1038/nprot.2014.174. Epub 2014 Oct 16.

20.

A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays.

Xiao Y, Segal MR, Yang YH, Yeh RF.

Bioinformatics. 2007 Jun 15;23(12):1459-67. Epub 2007 Apr 25.

PMID:
17459966

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